Current Computer - Aided Drug Design - Volume 17, Issue 4, 2021

Background: For the past several decades, the presence of tuberculosis (TB) is being remarked as the most common infectious disease leading to mortality. Objective: Hydrazone containing azometine group (-NHN=CH-) compounds have been reported for a broad range of bioactivities such as antiplatelet, analgesic, anti-inflammatory, anticonvulsant, antidepressant, antimalarial, vasodilator, antiviral, and antimicrobial, etc. Methods: For the synthesis of compounds (4a-4d) and (6a-6e), aromatic amines were treated with methyl terephthalaldehydate in methanol, giving Schiff’s bases, followed by reductive amination and further treatment with hydrazine hydrate gave acid hydrazides (4a-4d). These acid hydrazides were then treated with different aromatic aldehydes to yield hydrazones (6a-6d). All the synthesized compounds were subjected to FT-IR, NMR, and UV spectroscopic characterization. Results: Compounds (4a-4d) and (6a-6e) were found to have highly potent activity against Mycobacteria tuberculosis (Vaccine strain, H37 RV strains): ATCC No- 27294 (MIC:1.6-6.25 μg/mL) than standard anti-TB drugs. The compounds exhibited good radical scavenging potentials(0- 69.2%), as checked from DPPH protocol. All compounds also demonstrated good in-silico ADMET results. Conclusion: The current study revealed promising in vitro anti-tuberculosis and anti-oxidant profiles of hydrazide-hydrazone analogues.

Objective: The main objective of the study was to develop the Quantitative Structure- Activity Relationship (QSAR) and pharmacophore model by using data obtained from HT-29 cells to develop potent lead molecule for the scientific community. Materials and Methods: Common pharmacophore model, atom-based 3D-QSAR, and molecular dynamic (MD) simulation were carried out via computational techniques by using 4H-chromene derivatives. Results: The reliable common pharmacophoric hypothesis, DHH13 was generated and 3.95 survival value was also found. Furthermore, the statistically significant 3D-QSAR model was developed where r²=0.52 was found by using the Partial least squares (PLS) regression method. Phase predicted activity and Log GI50 demonstrated an important atomic position in the structure of ligands to ascertain anti colon cancer activity. Also, MD simulation was carried out between top rank leads targeting IL-6 that provided better binding conformational and complex stability into the active pocket site of the target throughout the MD simulation. Conclusion: The outcome of this design shows that the pharmacophore model and 3D-QSAR might be helpful for researchers in the field of medicinal chemistry to design and develop potential anti colon cancer compounds.

Introduction: Tyrosine threonine kinase (TTK1) is a key regulator of chromosome segregation. Recently, TTK targeting came into focus for the enhancement of possible anticancer therapies. Objective: In this regard, we employed our well-known method of QSAR-guided selection of the best crystallographic pharmacophore(s) to discover considerable binding interactions that transfer inhibitors into TTK1 binding site. Methods: Sixty-one TTK1 crystallographic complexes were used to extract 315 pharmacophore hypotheses. QSAR modeling was subsequently used to choose a single crystallographic pharmacophore that, when combined with other physicochemical descriptors, elucidates discrepancy in bioactivity of 55 miscellaneous inhibitors. Results: The best QSAR model was robust and predictive (r2(55) = 0.75, r2LOO = 0.72 , r2press against external testing list of 12 compounds = 0.67), Standard error of estimate (training set) (S)= 0.63 , Standard error of estimate (testing set)(Stest) = 0.62. The resulting pharmacophore and QSAR models were used to scan the National Cancer Institute (NCI) database for new TTK1 inhibitors. Conclusion: Five hits confirmed significant TTK1 inhibitory profiles with IC50 values ranging between 11.7 and 76.6 mM.

Introduction: In many diseased states, especially fibrosis and cancer, TGF-β family members are overexpressed and the outcome of signaling is diverted toward disease progression. As the result of activin receptor-like kinase 1 (ALK1) plays a key role in TGF-β signaling, discovering inhibitors of ALK1 to block TGF-β signaling for a therapeutic benefit has become an effective strategy. Methods: In this work, ZINC15894217 and ZINC12404282 were identified as potential ALK1 inhibitors using molecular docking, molecular dynamics simulation and MM/PBSA calculations studies. The analysis of energy decomposition found that Val208, Val216, Lys229, Gly283, Arg334 and Leu337 acted as crucial residues for ligand binding and system stabilizing. Results: In addition, these compounds displayed excellent pharmacological and structural properties, which can be further evaluated through in vitro and in vivo experiments for the inhibition of ALK1 to be developed as drugs against fibrosis and tumor. Conclusion: Overall, our study illustrated a time- and cost-effective computer aided drug design procedure to identify potential ALK1 inhibitors. It would provide useful information for further development of ALK1 inhibitors to improve disease related to TGF-β signal pathway.

Introduction: Inhibition of the reverse transcriptase (RT) enzyme of the human immunodeficiency virus (HIV) by low molecular weight inhibitors is still an active area of research. Here, protein-ligand interactions and possible binding modes of novel compounds with the HIV-1 RT binding pocket (the wild-type as well as Y181C and K103N mutants) were obtained and discussed. Methods: A molecular fragment-based approach using FDA-approved drugs were followed to design novel chemical derivatives using delavirdine, efavirenz, etravirine and rilpivirine as the scaffolds. The drug-likeliness of the derivatives was evaluated using Swiss-ADME. The parent molecule and derivatives were then docked into the binding pocket of related crystal structures (PDB ID: 4G1Q, 1IKW, 1KLM and 3MEC). Genetic Optimization for Ligand Docking (GOLD) Suite 5.2.2 software was used for docking and the results analyzed in the Discovery Studio Visualizer 4. A derivative was chosen for further analysis, if it passed drug-likeliness and the docked energy was more favorable than that of its parent molecule. Out of the fifty-seven derivatives, forty-eight failed in drug-likeness screening by Swiss-ADME or at the docking stage. Results: The final results showed that the selected compounds had higher predicted binding affinities than their parent scaffolds in both wild-type and the mutants. Binding energy improvement was higher for the structures designed based on second-generation NNRTIs (etravirine and rilpivirine) than the first-generation NNRTIs (delavirdine and efavirenz). For example, while the docked energy for rilpivirine was -51 KJ/mol, it was improved for its derivatives RPV01 and RPV15 up to - 58.3 and -54.5 KJ/mol, respectively. Conclusion: In this study, we have identified and proposed some novel molecules with improved binding capacity for HIV RT using a fragment-based approach.

Introduction: Lactoperoxidase (LPO) is a member of the mammalian heme peroxidase family and is an enzyme of the innate immune system. It possesses a covalently linked heme prosthetic group (a derivative of protoporphyrin IX) in its active site. LPO catalyzes the oxidation of halides and pseudohalides in the presence of hydrogen peroxide (H2O2) and shows a broad range of the antimicrobial activity. Methods: In this study, we have used two pharmaceutically important drug molecules, namely dapsone and propofol, which were earlier reported as potent inhibitors of LPO. At the same time, the stereochemistry and mode of binding of dapsone and propofol to LPO are still not known because of the lack of the crystal structures of LPO with these two drugs. In order to fill this gap, we utilized molecular docking and molecular dynamics (MD) simulation studies of LPO in its native and complex forms with dapsone and propofol. Results: From the docking results, the estimated binding free energies (ΔG) of -9.25 kcal/mol (Ki = 0.16 μM) and -7.05 kcal/mol (Ki = 6.79 μM) were observed for dapsone, and propofol, respectively. The standard error of the Auto Dock program is 2.5 kcal/mol; therefore, molecular docking results alone were inconclusive. Conclusion: To further validate the docking results, we performed MD simulation on unbound, and two drugs bounded LPO structures. Interestingly, MD simulations results explained that the structural stability of LPO-Propofol complex was higher than LPO-Dapsone complex. The results obtained from this study establish the mode of binding and interaction pattern of the dapsone and propofol to LPO as inhibitors.

Background: Coumarin is a fused ring system and possesses the enormous capability of targeting various receptors participating in the cancer pathway. Coumarin and its derivatives were found to exhibit very rare toxicity and other side effects. It has been found its immense anticancer potential depends on the nature of the group present and its pattern of substitution on the basic nucleus. Objectives: Synthesis of C-4 substituted coumarin derivatives and to study their molecular interactions with ERα for the anticancer activity for Breast Cancer. Methods: C-4 substituted coumarins analogues (1-10) have been synthesized using conventional heating and microwave irradiation. Using Schrodinger software, molecular modeling studies were carried out and ADME properties of the compounds were predicted. Results: All the synthesized compounds have shown better G-Score (-6.87 to -8.43 kcal/mol) as compared to the standard drug tamoxifen (-5.28kcal/mol) and auraptene (-3.89kcal/mol). Molecular docking suggests that all compounds fit in the active site of protein as they have the same hydrophobic pocket as standard drug tamoxifen, and have an acceptable range of ADME properties. Conclusion: Microwave-assisted synthesis showed better results as compared to conventional heating. In silico studies revealed that all the compounds befit in the active site of the protein. ADME properties showed that all compounds are in allowable limits for human oral absorption. In the future, there is a possibility of in vitro and in vivo studies of the synthesized compounds.

Introduction: Cycloxygenase I (COX I) plays an important role in the pathogenesis of atherothrombosis. Therefore, there is a need of anti-platelet aggregation drugs that decrease thrombus formation. Methods: Molecular docking of the phytochemicals (flavonoids, alkaloids, terpenoids and lignans) was carried out. Binding energies and the ligand efficiencies of the phytochemicals were compared by standard statistical tool. Results: Docking showed that their inhibitory activity towards COX I mainly depends on hydrogen bonds between the hydroxyl groups of the polyphenol ligands and the binding sites, π-cation/anion, π-sigma bond, π-alkyl, and π-π T shaped interactions that stabilize the ligand within the active site. Alkaloids are superior over the others to develop as optimal inhibitor compounds of human COX I in terms of ligand efficiency. Conclusion: Ligand efficiencies fall within the criteria of orally efficacious drugs, and could pave a way for lead anti-platelet drug discovery and subsequent development.

Background: Plasmodium falciparum is the most dangerous and widespread diseasecausing species of malaria. Falcipain-2 (FP2) of Plasmodium falciparum, is a potential target for antimalarial chemotherapy since it is involved in an essential cellular function such as hemoglobin degradation during the parasite’s life cycle. However, despite their central role in the life cycle of the parasite, no commercial drug targeting Falcipain-2 has been developed to date. Prior efforts to develop peptide-based drugs against Plasmodium have been futile due to their susceptibility to being degraded by host enzymes. Objective: Here, we report computer-aided drug design of new nonpeptidic inhibitors against FP2, which are likely to be safe from degradation by host enzymes. Methods: We have virtually screened for the probable FP2 inhibitors from the PubChem database by submitting the well-equilibrated 3-D structure of FP2. Furthermore, virtual screenings and dockings were carried out using PyRx and Discovery Studio. Results: We found 15 top-ranking molecules with carbaldehyde pharmacophore having a good fit with the target protein. Based on the C-Docker values, the top 4 hits (PubChem 44138738, Pub- Chem 20983198, PubChem 20983081 and PubChem 28951461) for FP2 were identified. These four hits have been observed to bound to the active cleft of the protein. Moreover, their complexes were also found to be stable from the RMSD and Radius of Gyration analysis. Conclusion: The selected compounds 2-(benzylamino)-8-methylquinoline-3-carbaldehyde (Pub- Chem44138738), 6-bromo-2-(3,4-dihydro-1H-isoquinolin-2-yl)quinoline-3-carbaldehyde (Pub- Chem 20983198), 2-(3,4-dihydro-1H-isoquinolin-2-yl)-6-ethylquinoline-3-carbaldehyde(PubChem 20983081)and 2-[benzyl(methyl)amino]quinoline-3-carbaldehyde (PubChem 28951461) may be the starting point for further modification as a new type of nonpeptidic drug for malaria disease.

Background: Euterpe oleracea Martius, popularly known as açaí, is a fruit rich in α- tocopherols, fibers, lipids, mineral ions, and polyphenols. It is believed that the high content of polyphenols, especially flavonoids, provides several health-promoting effects to the açaí fruit, including anti-inflammatory, immunomodulatory, antinociceptive and antioxidant properties. Most of the flavonoids are antioxidant molecules of plant origin that act as a trap for free radicals, reacting and neutralizing them, thus offering perspectives in preventing oxidative damage. Objective: In this study, we aim to perform an in silico evaluation of flavonoids present in the pulp and the oil of Euterpe oleracea Martius, evaluating their potential to serve as antioxidant agents. Methods: Firstly, we selected 16 flavonoids present in Euterpe oleracea Martius pulp and oil, and then their physicochemical properties were analyzed concerning the Lipinski’s Rule of Five. Moreover, we evaluated their pharmacokinetic properties using the QikProp module of the Schrödinger software as well as their toxicity profile, using the DEREK software. Docking simulations, using the GOLD 4.1 software, as well as pharmacophoric hypotheses calculation of molecules were also performed. Results: Flavonoids present in the açaí pulp including catechin, epicatechin, luteolin, chrisoeriol, taxifolin, apigenin, dihydrokaempferol, isovitexin, and vitexin presented good oral bioavailability. Regarding the pharmacokinetic properties, the compounds catechin, epicatechin, isovitexin, luteolin, chrisoeriol, taxifolin, and isorhamnetin rutinoside presented the best results, besides high human oral absorption. Regarding the prediction of toxicological properties, compounds isorhamnetin rutinoside and rutin presented mutagenicity for hydroxynaphthalene or derivate, and regarding the docking simulations, all the compounds investigated in this study presented key interactions with the corresponding targets. Conclusion: The flavonoids catechin, chrysoeriol, and taxifolin presented the best results according to the evaluation conducted in this study. These computational results can be used as a theoretical basis for future studies concerning the development of drug candidates, as well as to enlighten biological tests in vitro and in vivo, which can contribute to the treatment of neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, and Huntington's disease.